.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.8.
.TH KRAKEN2-BUILD "1" "March 2019" "kraken2-build 2.0.7~beta" "User Commands"
.SH NAME
kraken2-build \- assigning taxonomic labels to short DNA sequences
.SH SYNOPSIS
.B kraken2-build
[\fI\,task option\/\fR] [\fI\,options\/\fR]
.SH DESCRIPTION
.SS "Task options (exactly one must be selected):"
.TP
\fB\-\-download\-taxonomy\fR
Download NCBI taxonomic information
.TP
\fB\-\-download\-library\fR TYPE
Download partial library
(TYPE = one of "archaea", "bacteria", "plasmid",
"viral", "human", "fungi", "plant", "protozoa",
"nr", "nt", "env_nr", "env_nt", "UniVec",
"UniVec_Core")
.TP
\fB\-\-special\fR TYPE
Download and build a special database
(TYPE = one of "greengenes", "silva", "rdp")
.TP
\fB\-\-add\-to\-library\fR FILE
Add FILE to library
.TP
\fB\-\-build\fR
Create DB from library
(requires taxonomy d/l'ed and at least one file
in library)
.TP
\fB\-\-clean\fR
Remove unneeded files from a built database
.TP
\fB\-\-standard\fR
Download and build default database
.TP
\fB\-\-help\fR
Print this message
.TP
\fB\-\-version\fR
Print version information
.SH OPTIONS
.TP
\fB\-\-db\fR NAME
Kraken 2 DB/library name (mandatory except for
\fB\-\-help\fR/\-\-version)
.TP
\fB\-\-threads\fR #
Number of threads (def: 1)
.TP
\fB\-\-kmer\-len\fR NUM
K\-mer length in bp/aa (build task only;
def: 35 nt, 15 aa)
.TP
\fB\-\-minimizer\-len\fR NUM
Minimizer length in bp/aa (build task only;
def: 31 nt, 15 aa)
.TP
\fB\-\-minimizer\-spaces\fR NUM
Number of characters in minimizer that are
ignored in comparisons (build task only;
def: 6 nt, 0 aa)
.TP
\fB\-\-protein\fR
Build a protein database for translated search
.TP
\fB\-\-no\-masking\fR
Used with \fB\-\-standard\fR/\-\-download\-library/
\fB\-\-add\-to\-library\fR to avoid masking low\-complexity
sequences prior to building; masking requires
dustmasker or segmasker to be installed in PATH,
which some users might not have.
.TP
\fB\-\-max\-db\-size\fR NUM
Maximum number of bytes for Kraken 2 hash table;
if the estimator determines more would normally be
needed, the reference library will be downsampled
to fit. (Used with \fB\-\-build\fR/\-\-standard/\-\-special)
.SH AUTHOR
This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.